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I build a CNN 1d Autoencoder in Keras, following the advice in this SO question, where Encoder and Decoder are separated. My goal is to re-use the decoder, once the Autoencoder has been trained. The central layer of my Autoencoder is a Dense layer, because I would like to learn it afterwards.

My problem is that if I compile and fit the whole Autoencoder, written as Decoder()Encoder()(x) where x is the input, I get a different prediction when I do

autoencoder.predict(training_set)

w.r.t. if I first encode the training set in a set of central features, and then let the decoder decode them. These two approaches should give identical answers, once the Autoencoder has been trained.

from tensorflow.keras.layers import Input, Dense, BatchNormalization, Flatten, Lambda, Activation, Conv1D, MaxPooling1D, UpSampling1D, Reshape
from tensorflow.keras.models import Model
from tensorflow.keras import optimizers
from tensorflow.keras.layers import GaussianNoise
import keras.backend as K
from tensorflow.keras.layers import Add

import tensorflow as tf

import scipy.io
import sys
import matplotlib.pyplot as plt
import numpy as np
import copy


training = # some training set, 1500 samples of 501 point each
testing = # some testing set, 500 samples of 501 point each

# reshaping for CNN
training = np.reshape(training, [1500, 501, 1])
testing = np.reshape(testing, [500, 501, 1])


# normalize input
X_mean = training.mean()
oscillations -= X_mean
X_std = training.std()
training /= X_std


copy_of_test = copy.copy(testing)
testing -= X_mean
testing /= X_std

### MODEL ###

def Encoder():
    encoder_input = Input(batch_shape=(None, 501, 1))  
    e1 = Conv1D(256,3, activation='tanh', padding='valid')(encoder_input)
    e2 = MaxPooling1D(2)(e1)
    e3 = Conv1D(32,3, activation='tanh', padding='valid')(e2)
    e4 = MaxPooling1D(2)(e3)
    e5 = Flatten()(e4)
    encoded = Dense(32,activation = 'tanh')(e5)
    return Model(encoder_input, encoded)


def Decoder():
    encoded_input = Input(shape=(32,))  
    encoded_reshaped = Reshape((32,1))(encoded_input)
    d1 = Conv1D(32, 3, activation='tanh', padding='valid', name='decod_conv1d_1')(encoded_reshaped)
    d2 = UpSampling1D(2, name='decod_upsampling1d_1')(d1)
    d3 = Conv1D(256, 3, activation='tanh', padding='valid', name='decod_conv1d_2')(d2)
    d4 = UpSampling1D(2, name='decod_upsampling1d_2')(d3)
    d5 = Flatten(name='decod_flatten')(d4)
    d6 = Dense(501, name='decod_dense1')(d5)
    decoded = Reshape((501,1), name='decod_reshape')(d6)
    return Model(encoded_input, decoded)


# define input to the model:
x = Input(batch_shape=(None, 501, 1))
y = Input(shape=(32,))

# make the model:
autoencoder = Model(x, Decoder()(Encoder()(x)))

# compile the model:
autoencoder.compile(optimizer='adam', loss='mse')
for layer in autoencoder.layers: print(K.int_shape(layer.output))


epochs = 100
batch_size = 100
validation_split = 0.2
# train the model
history = autoencoder.fit(x = training, y = training,
                    epochs=epochs,
                    batch_size=batch_size,
                    validation_split=validation_split)

# Encoder
encoder = Model(inputs=x, outputs=Encoder()(x), name='encoder')
print('enc:')
for layer in encoder.layers: print(K.int_shape(layer.output))
features = encoder.predict(training) # features

# Decoder
decoder = Model(inputs=y, outputs=Decoder()(y), name='decoder')
print('dec:')
for layer in decoder.layers: print(K.int_shape(layer.output))
score = decoder.predict(features) # 
score = np.squeeze(score)    

predictions = autoencoder.predict(training)
predictions = np.squeeze(predictions)

# plotting one random case
# score should be equal to predictions!
# because score is obtained from the trained decoder acting on the encoded features, while predictions are obtained form the Autoencoder acting on the training set 
plt.plot(score[100], label='eD')
plt.plot(predictions[100], label='AE')
plt.legend()
plt.show()
plt.close()
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When you do autoencoder.fit, your model is learning something so your weights are changing for the encoder model and decoder model. After that while creating your encoder/Decoder like "encoder = Model(inputs=x, outputs=Encoder()(x), name='encoder')", you are creating another encoder model with differnt weights, you have to use the same weight vectors. Check "autoencoder.layers[1].get_weights()" is equal to "encoder.get_weights()" or not, then you will get to know what is happening in the model.( similar thing for decoder as well). You can check that using below code,

for i in range(len(autoencoder.layers[1].weights)):
    print((autoencoder.layers[1].get_weights()[i]==encoder.get_weights()[i]).all())
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